I have something similar to this in Lion since I bought my Mac. Except, the programs had to be opened at one point for me. I could open the program, then close out of it, no light under the icon in the dock or icon completely gone from the dock, appears to be completely off. Yet when I look at the "Force Quit App" list, they will appear in there. In order for me to close QT or Preview, I have to force quit them. Very annoying. Although it has put me in the habit of hitting CMD+Q a lot more now.